House cleaning, a part of good housekeeping

Abstract

SummaryCellular metabolism constantly generates by-products that are wasteful or even harmful. Such compounds are excreted from the cell or are removed through hydrolysis to normal cellular metabolites by various 'house-cleaning' enzymes. Some of the most important contaminants are non-canonical nucleoside triphosphates (NTPs) whose incorporation into the nascent DNA leads to increased mutagenesis and DNA damage. Enzymes intercepting abnormal NTPs from incorporation by DNA polymerases work in parallel with DNA repair enzymes that remove lesions produced by modified nucleotides. House-cleaning NTP pyrophosphatases targeting non-canonical NTPs belong to at least four structural superfamilies: MutTrelated (Nudix) hydrolases, dUTPase, ITPase (Maf/ HAM1) and all-α α α α NTP pyrophosphatases (MazG). These enzymes have high affinity ( K m 's in the micromolar range) for their natural substrates (8-oxo-dGTP, dUTP, dITP, 2-oxo-dATP), which allows them to select these substrates from a mixture containing a ∼ ∼ ∼ ∼ 1000-fold excess of canonical NTPs. To date, many housecleaning NTPases have been identified only on the basis of their side activity towards canonical NTPs and NDP derivatives. Integration of growing structural and biochemical data on these superfamilies suggests that their new family members cleanse the nucleotide pool of the products of oxidative damage and inappropriate methylation. House-cleaning enzymes, such as 6-phosphogluconolactonase, are also part of normal intermediary metabolism. Genomic data suggest that house-cleaning systems are more abundant than previously thought and include numerous analogous enzymes with overlapping functions. We discuss the structural diversity of these enzymes, their phylogenetic distribution, substrate specificity and the problem of identifying their true substrates.'Heal thyself' Ascribed to Hippocrates, V century BC

Crystal Structure of Human Inosine Triphosphatase

“…At the high concentration used, binding of the nonphysiological ATP analog presumably took place at a secondary or artificial site in the Methanococcus enzyme. We suggest that the substrate binding site revealed in our human ITPA structure, which has recently been predicted by Murzin and co-workers (15), is conserved across this enzyme family.…”

“…Crystal structures of several bacterial ITPA homologs have been solved in the absence of physiological ligands (13)(14)(15). The location of the substrate binding site has been postulated on the basis of weak binding of the non-physiological ATP analog, AMPPNP, to the Methanococcus enzyme (13).…”

ITPase-deficient mice show growth retardation and die before weaning

“…32 To clarify the biological significance of the damaged nucleotides and the enzymes that eliminate them, we produced and analyzed KO mice which lack sanitizing enzyme activity. Here, we have produced and analyzed ITPase-deficient (Itpa À/À ) mice.…”

Cross-species inhibition of dUTPase via the Staphylococcal Stl protein perturbs dNTP pool and colony formation in Mycobacterium

“…Preventive DNA repair relies on dNTP pool sanitizing pathways, among which dUTPase enzymes catalyse pyrophosphorolysis of dUTP generating dUMP and inorganic pyrophosphate [3,11,12]. This reaction is of key importance since dUTP is constantly produced in the pyrimidine biosynthesis pathways and most (including mycobacterial) DNA polymerases readily incorporate dUMP into DNA as a dTMP replacement if the cellular dUTP pool is elevated.…”